Because dielectrics between active layers have low thermal conductivities, there is a demand to reduce the temperature increase in three-dimensional integrated circuits (3D ICs). This paper demonstrates that, in the design of 3D ICs, different layer assignments often lead to different temperature increases. Based on this observation, we are motivated to perform temperature-aware layer assignment. Our work includes two parts. Firstly, an integer linear programming (ILP) approach that guarantees a minimum temperature increase is proposed. Secondly, a polynomial-time heuristic algorithm that reduces the temperature increase is proposed. Compared with the previous work, which does not take the temperature increase into account, the experimental results show that both our ILP approach and our heuristic algorithm produce a significant reduction in the temperature increase with a very small area overhead.